HIV Drug Resistance Database
Stanford University HIV Drug Resistance Database - A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance.

Genotype-Rx Datasets

2013-4-29

Genotype-rx correlaton datasets include all publicly available HIV-1 isolates in HIVdb and the lists of ARVs (antiretrovials) received prior to the isolations.

GeneDatasetNumber of isolates includedDescription
proteasePR.txt65,628 isolates
from 59,982 persons, 663 references
protease isolates and the lists of protease inhibitors received
RTRT.txt68,482 isolates
from 62,136 persons, 664 references
RT isolates and the lists of RT inhibitors received
integraseIN.txt6,219 isolates
from 5,939 persons, 235 references
integrase isolates and the lists of integrase inhibitors received
Note: (a) isolates with unknown treatment status were excluded; (b) isolates obtained from CPZ were excluded; (c) only a consensus amino acid sequence was included if an isolate was cloned; (d) primary references from which the isolates were descrived can be found Ref.txt; (e) suggested citation can be found on FAQ page.

Description of fields in the datasets (fields are tab-delimited.)

Field NameDescription
RefIDReference identifier;linked to Ref.txt
PtIDPatient identifier
IsolateNameIsolate identifier
RegionRegion of sampling;
YearYear of sampling; preceded by '=' when the exact year of sampling is available or '<' otherwise
SubtypeSubtype of sequence; 'NA' if subtype could not be classifed because nucleotide sequence was not available; 'Others' if the subtype of sequence is a circulating recombinant form other than CRF01_AE and CRF02_AG or a non-CRF recombinant or other non-classifiable group M sequence.
PIList (or RTIList or INIList)List of protease (or RT or integrase) inhibitors received prior to sequencing; 'None' when no ARVs received; 'Unknown' when an ARV was received or not is not known; 'PI' when a protease inhibitor was received but which protease inhibitor was recceived is not known; 'NRTI' when a NRTI was received but which NRTI was received is not known; 'NNRTI' when a NNRTI was received but which NNRTI was received is not known; 'RTI' when a RTI (either NRTI or NNRTI) was received but which RTI was received is not known
P1...PnAmino acid at this position. '-' indicates consensus; '.' indicates no sequence; '#' indicates an insertion; '~' indicates a deletion; '*' indicates a stop codon and a letter indicates one letter Amino Acid substitution. Two and more amino acid codes indicates a mixture. The consensus B amino acid sequences can be found here.
AccessionIDGenbank AccessionID number
NASeqNucelotide sequence